TB-Profiler result

Run: ERR4827811

Summary

Run ID: ERR4827811

Sample name:

Date: 01-04-2023 18:21:59

Number of reads: 5415527

Percentage reads mapped: 98.21

Strain: lineage4.8;lineage4.3.3

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 0.29
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.73
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.29
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
pncA 2289162 p.Leu27Pro missense_variant 0.28 pyrazinamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.27
gyrA 8040 p.Gly247Ser missense_variant 0.34
gyrA 9304 p.Gly668Asp missense_variant 0.31
mshA 576108 p.Ala254Gly missense_variant 0.28
rpoC 764995 c.1626C>G synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.73
rpsA 1834836 p.Met432Thr missense_variant 0.24
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.33
PPE35 2168149 p.Pro822Ser missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.33
folC 2746340 p.Ala420Val missense_variant 0.29
thyA 3073868 p.Thr202Ala missense_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 0.3
ald 3086987 p.Gln56His missense_variant 0.34
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.31
clpC1 4038287 c.2418C>T synonymous_variant 0.29
clpC1 4038968 c.1737G>A synonymous_variant 0.27
clpC1 4039729 p.Asp326Asn missense_variant 0.69
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246584 p.Arg24Pro missense_variant 0.48
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.28